7VGW

Yeast gid10 with Pro-peptide

Summary for 7VGW

• Entry DOI: 10.2210/pdb7vgw/pdb
• Descriptor: BJ4_G0041530.mRNA.1.CDS.1 (1 entity in total)
• Functional Keywords: ubiquitination, n-degron, e3 ligase, pro-n end rule., unknown function
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Total number of polymer chains: 2
• Total formula weight: 55381.48

Authors

Shin, J.S.,Park, S.H.,Kim, L.,Heo, J.,Song, H.K. (deposition date: 2021-09-19, release date: 2022-07-27, Last modification date: 2023-11-29)

Primary citation

Shin, J.S.,Park, S.H.,Kim, L.,Heo, J.,Song, H.K.
Crystal structure of yeast Gid10 in complex with Pro/N-degron.
Biochem.Biophys.Res.Commun., 582:86-92, 2021

PubMed Abstract: The cellular glucose level has to be tightly regulated by a variety of cellular processes. One of them is the degradation of gluconeogenic enzymes such as Fbp1, Icl1, Mdh2, and Pck1 by GID (glucose-induced degradation deficient) E3 ubiquitin ligase. The Gid4 component of the GID ligase complex is responsible for recognizing the N-terminal proline residue of the target substrates under normal conditions. However, an alternative N-recognin Gid10 controls the degradation process under stressed conditions. Although Gid10 shares a high sequence similarity with Gid4, their substrate specificities are quite different. Here, we report the structure of Gid10 from Saccharomyces cerevisiae in complex with Pro/N-degron, Pro-Tyr-Ile-Thr, which is almost identical to the sequence of the natural substrate Art2. Although Gid10 shares many structural features with the Gid4 protein from yeast and humans, the current structure explains the unique structural difference for the preference of bulky hydrophobic residue at the second position of Pro/N-degron. Therefore, this study provides a fundamental basis for understanding of the structural diversity and substrate specificity of recognition components in the GID E3 ligase complex involved in the Pro/N-degron pathway.

PubMed: 34695755
DOI: 10.1016/j.bbrc.2021.10.007

Experimental method

X-RAY DIFFRACTION (2.8 Å)